Background:: The frequency of invasive opportunistic mycoses has increased significantly over the past decades especially in immunocompromised patients. Invasive aspergillosis (IA) has become a major cause of morbidity and mortality among these patients. As bronchoalveolar lavage (BAL) fluid samples are generally useful specimens in the diagnosis of invasive pulmonary aspergillosis (IPA), this study was designed to evaluate the incidence of fungal elements in at-risk patients by direct microscopy and culture of BAL samples. Methods:: In a 16-month period, 400 BAL samples were obtained from several groups of different patients with pulmonary and respiratory disorders and examined by using both direct microscopy and culture. Results:: Of the 400 samples, 16 (4%) were positive direct examination with branching septate hyphae and 46 (11.5%) were positive culture: 25 (54%) Aspergillus flavus, 6 (13%) A. fumigatus, 5 (10.9%) A. niger, 1 (2.2%) A. terreus, 3 (6.5%) Penicillium spp. and 6 (13%) mixed A. flavus/A. niger. A. flavus was the most common cause of Aspergillus infection or colonization. Bone marrow transplant (BMT) recipients were the most susceptible group to fungal infection and/or colonization. Conclusion:: Among Aspergillus species, A. flavus was the most common isolate in both infections and colonization in Iran. More studies are needed to clarify the epidemiological aspect of aspergillosis in Iran.